Identifying remote protein homologs by network propagation

William Stafford Noble, Rui Kuang, Christina Leslie and Jason
Weston

FEBS Journal. 272(20):5119-5128, 2005.

Abstract

Perhaps the most widely used applications of bioinformatics are tools
such as PSI-BLAST for searching sequence databases. We describe a
recently developed protein database search algorithm called RankProp.
RankProp relies upon a pre-computed network of protein pairwise
similarities. The algorithm performs a diffusion operation from a
specified query protein across the protein similarity network. The
resulting activation scores, assigned to each database protein, encode
information about the global structure of the protein similarity
network. This type of algorithm has a rich history in associationist
psychology, artificial intelligence and web search. We describe the
RankProp algorithm and its relatives, and we provide evidence that the
algorithm successfully improves upon the rankings produced by
PSI-BLAST.
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